SMTL ID : 1jz7.1

E. COLI (lacZ) BETA-GALACTOSIDASE IN COMPLEX WITH GALACTOSE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

8 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.1: 13 residues within 4Å: Chain A: N.102, D.201, H.391, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604 Ligands: NA.6 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.391, A:N.460, A:E.461, A:F.601, A:N.604 Water bridges: A:N.102, A:D.201, A:D.201, A:D.201 GAL.2: 8 residues within 4Å: Chain A: D.659, Q.693, W.695, R.721, E.724, F.915, R.942 Chain B: R.1013 15 PLIP interactions: 7 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:Q.693, A:R.721, A:R.721, A:E.724, A:R.942 Water bridges: A:R.942, B:E.871, B:S.874, B:R.1013, B:R.1013, B:R.1013, B:R.1013, B:R.1013 Salt bridges: A:R.942, B:R.1013 GAL.34: 13 residues within 4Å: Chain B: N.102, D.201, H.391, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, N.604, W.999 Ligands: NA.38 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:D.201, B:H.391, B:N.460, B:E.461, B:E.461, B:F.601, B:N.604 Water bridges: B:N.102, B:D.201, B:D.201, B:D.201, B:H.418 GAL.35: 9 residues within 4Å: Chain A: S.874, R.1013 Chain B: D.659, Q.693, W.695, R.721, E.724, F.915, R.942 16 PLIP interactions: 7 interactions with chain A, 9 interactions with chain B Water bridges: A:S.874, A:R.1013, A:R.1013, A:R.1013, A:R.1013, A:R.1013, B:R.942, B:R.942 Salt bridges: A:R.1013, B:R.942 Hydrogen bonds: B:D.659, B:Q.693, B:R.721, B:R.721, B:E.724, B:R.942 GAL.65: 13 residues within 4Å: Chain C: N.102, D.201, H.391, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604 Ligands: NA.70 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:D.201, C:H.391, C:N.460, C:E.461, C:Y.503, C:F.601 Water bridges: C:N.102, C:N.102, C:D.201, C:D.201, C:D.201, C:E.461 GAL.66: 8 residues within 4Å: Chain C: D.659, Q.693, W.695, R.721, E.724, F.915, R.942 Chain D: R.1013 16 PLIP interactions: 8 interactions with chain C, 8 interactions with chain D Hydrogen bonds: C:D.659, C:R.721, C:R.721, C:E.724, C:R.942 Water bridges: C:R.942, C:R.942, D:R.1013, D:R.1013, D:R.1013, D:R.1013, D:R.1013, D:R.1013, D:R.1013 Salt bridges: C:R.942, D:R.1013 GAL.98: 12 residues within 4Å: Chain D: N.102, D.201, H.391, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, N.604 Ligands: NA.103 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:H.391, D:N.460, D:E.461 Water bridges: D:N.102, D:D.201, D:D.201, D:D.201 GAL.99: 8 residues within 4Å: Chain C: R.1013 Chain D: D.659, Q.693, W.695, R.721, E.724, F.915, R.942 20 PLIP interactions: 10 interactions with chain D, 10 interactions with chain C Hydrogen bonds: D:D.659, D:Q.693, D:R.721, D:R.721, D:E.724, D:R.942 Water bridges: D:E.724, D:E.724, D:R.942, C:S.874, C:R.1013, C:R.1013, C:R.1013, C:R.1013, C:R.1013, C:R.1013, C:R.1013, C:R.1013 Salt bridges: D:R.942, C:R.1013

15 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 3 residues within 4Å: Chain A: E.416, H.418, E.461 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.416, A:H.418, A:E.461, H2O.1, H2O.3, H2O.6 MG.4: 6 residues within 4Å: Chain A: D.15, N.18, V.21, Y.161, Q.163, D.193 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.15, A:N.18, A:V.21, A:D.193, A:D.193 MG.5: 1 residues within 4Å: Ligands: DMS.16 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain A: N.597, E.797 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:N.597, H2O.9, H2O.17, H2O.19, H2O.23 MG.36: 4 residues within 4Å: Chain B: N.102, E.416, H.418, E.461 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.416, B:H.418, B:E.461, H2O.42, H2O.45, H2O.47 MG.37: 6 residues within 4Å: Chain B: D.15, N.18, V.21, Y.161, Q.163, D.193 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.15, B:N.18, B:V.21, B:D.193, B:D.193 MG.42: 1 residues within 4Å: Chain B: N.597 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:N.597, H2O.50, H2O.58, H2O.60, H2O.64, H2O.79 MG.67: 3 residues within 4Å: Chain C: E.416, H.418, E.461 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.416, C:H.418, C:E.461, H2O.84, H2O.86, H2O.89 MG.68: 5 residues within 4Å: Chain C: D.15, N.18, V.21, Q.163, D.193 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.15, C:N.18, C:V.21, C:D.193 MG.69: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.74: 1 residues within 4Å: Chain C: N.597 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:N.597, H2O.92, H2O.100, H2O.101, H2O.106 MG.100: 3 residues within 4Å: Chain D: E.416, H.418, E.461 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.416, D:H.418, D:E.461, H2O.124, H2O.126, H2O.129 MG.101: 5 residues within 4Å: Chain D: D.15, N.18, V.21, Q.163, D.193 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.15, D:N.18, D:V.21, D:D.193, D:D.193 MG.102: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.107: 1 residues within 4Å: Chain D: N.597 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:N.597, H2O.132, H2O.140, H2O.142, H2O.146

16 x NA: SODIUM ION(Non-functional Binders)

NA.6: 5 residues within 4Å: Chain A: Y.100, D.201, F.601, N.604 Ligands: GAL.1 Ligand excluded by PLIP NA.7: 4 residues within 4Å: Chain A: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.8: 5 residues within 4Å: Chain A: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.9: 4 residues within 4Å: Chain A: S.647, E.650, L.670 Ligands: DMS.29 Ligand excluded by PLIP NA.38: 5 residues within 4Å: Chain B: Y.100, D.201, F.601, N.604 Ligands: GAL.34 Ligand excluded by PLIP NA.39: 4 residues within 4Å: Chain B: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.40: 5 residues within 4Å: Chain B: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.41: 4 residues within 4Å: Chain B: S.647, E.650, L.670 Ligands: DMS.60 Ligand excluded by PLIP NA.70: 5 residues within 4Å: Chain C: Y.100, D.201, F.601, N.604 Ligands: GAL.65 Ligand excluded by PLIP NA.71: 4 residues within 4Å: Chain C: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.72: 5 residues within 4Å: Chain C: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.73: 4 residues within 4Å: Chain C: S.647, E.650, L.670 Ligands: DMS.93 Ligand excluded by PLIP NA.103: 5 residues within 4Å: Chain D: Y.100, D.201, F.601, N.604 Ligands: GAL.98 Ligand excluded by PLIP NA.104: 4 residues within 4Å: Chain D: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.105: 5 residues within 4Å: Chain D: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.106: 5 residues within 4Å: Chain D: S.647, N.649, E.650, L.670 Ligands: DMS.124 Ligand excluded by PLIP

91 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.11: 9 residues within 4Å: Chain A: T.229, V.330, G.331, R.333, R.448, N.449, H.450, P.451, R.482 Ligand excluded by PLIP DMS.12: 5 residues within 4Å: Chain A: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.13: 5 residues within 4Å: Chain A: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.14: 7 residues within 4Å: Chain A: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligand excluded by PLIP DMS.15: 4 residues within 4Å: Chain A: T.271, T.290, L.291, R.292 Ligand excluded by PLIP DMS.16: 5 residues within 4Å: Chain A: E.314, H.316, G.320, L.322 Ligands: MG.5 Ligand excluded by PLIP DMS.17: 4 residues within 4Å: Chain A: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.18: 4 residues within 4Å: Chain A: L.54, N.55, L.125, F.127 Ligand excluded by PLIP DMS.19: 5 residues within 4Å: Chain A: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.20: 3 residues within 4Å: Chain A: P.106, P.115, W.191 Ligand excluded by PLIP DMS.21: 5 residues within 4Å: Chain A: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.22: 6 residues within 4Å: Chain A: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.23: 3 residues within 4Å: Chain A: G.593, D.594, T.595 Ligand excluded by PLIP DMS.24: 3 residues within 4Å: Chain A: V.84, V.85, H.93 Ligand excluded by PLIP DMS.25: 2 residues within 4Å: Chain A: K.621, W.717 Ligand excluded by PLIP DMS.26: 2 residues within 4Å: Chain A: R.251, D.252 Ligand excluded by PLIP DMS.27: 4 residues within 4Å: Chain A: D.428, P.430 Chain D: W.474, V.478 Ligand excluded by PLIP DMS.28: 3 residues within 4Å: Chain A: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.29: 7 residues within 4Å: Chain A: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.9 Ligand excluded by PLIP DMS.30: 6 residues within 4Å: Chain A: A.34, W.36, D.45, R.46, P.47, S.48 Ligand excluded by PLIP DMS.31: 5 residues within 4Å: Chain A: E.57, W.58, R.59, L.125, T.126 Ligand excluded by PLIP DMS.32: 4 residues within 4Å: Chain A: Q.50, S.132, E.136, H.216 Ligand excluded by PLIP DMS.33: 5 residues within 4Å: Chain A: N.102, D.598, R.599, F.601, V.795 Ligand excluded by PLIP DMS.43: 8 residues within 4Å: Chain B: T.229, V.330, G.331, R.333, R.448, N.449, P.451, R.482 Ligand excluded by PLIP DMS.44: 5 residues within 4Å: Chain B: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.45: 5 residues within 4Å: Chain B: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.46: 7 residues within 4Å: Chain B: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligand excluded by PLIP DMS.47: 4 residues within 4Å: Chain B: T.271, T.290, L.291, R.292 Ligand excluded by PLIP DMS.48: 4 residues within 4Å: Chain B: E.314, H.316, G.320, L.322 Ligand excluded by PLIP DMS.49: 4 residues within 4Å: Chain B: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.50: 5 residues within 4Å: Chain B: L.54, N.55, E.57, W.58, L.125 Ligand excluded by PLIP DMS.51: 4 residues within 4Å: Chain B: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.52: 4 residues within 4Å: Chain B: I.99, P.106, P.115, W.191 Ligand excluded by PLIP DMS.53: 5 residues within 4Å: Chain B: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.54: 5 residues within 4Å: Chain B: G.275, G.276, V.289, T.290, R.292 Ligand excluded by PLIP DMS.55: 3 residues within 4Å: Chain B: V.84, V.85, H.93 Ligand excluded by PLIP DMS.56: 3 residues within 4Å: Chain B: L.250, R.251, D.252 Ligand excluded by PLIP DMS.57: 5 residues within 4Å: Chain B: F.231, N.232, D.233, F.235, E.334 Ligand excluded by PLIP DMS.58: 3 residues within 4Å: Chain B: D.428 Chain C: R.448, V.478 Ligand excluded by PLIP DMS.59: 3 residues within 4Å: Chain B: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.60: 7 residues within 4Å: Chain B: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.41 Ligand excluded by PLIP DMS.61: 5 residues within 4Å: Chain B: A.34, W.36, D.45, R.46, P.47 Ligand excluded by PLIP DMS.62: 5 residues within 4Å: Chain B: E.57, W.58, R.59, L.125, T.126 Ligand excluded by PLIP DMS.63: 6 residues within 4Å: Chain B: R.37, Q.50, S.132, W.133, E.136, H.216 Ligand excluded by PLIP DMS.64: 4 residues within 4Å: Chain B: V.267, N.294, V.295, E.296 Ligand excluded by PLIP DMS.75: 8 residues within 4Å: Chain C: T.229, V.330, G.331, R.333, R.448, N.449, P.451, R.482 Ligand excluded by PLIP DMS.76: 5 residues within 4Å: Chain C: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.77: 5 residues within 4Å: Chain C: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.78: 8 residues within 4Å: Chain C: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligands: DMS.94 Ligand excluded by PLIP DMS.79: 3 residues within 4Å: Chain C: T.271, L.291, R.292 Ligand excluded by PLIP DMS.80: 4 residues within 4Å: Chain C: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.81: 5 residues within 4Å: Chain C: L.54, N.55, G.56, E.57, L.125 Ligand excluded by PLIP DMS.82: 5 residues within 4Å: Chain C: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.83: 3 residues within 4Å: Chain C: P.106, P.115, W.191 Ligand excluded by PLIP DMS.84: 5 residues within 4Å: Chain C: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.85: 4 residues within 4Å: Chain C: G.275, V.289, T.290, R.292 Ligand excluded by PLIP DMS.86: 3 residues within 4Å: Chain C: G.593, D.594, T.595 Ligand excluded by PLIP DMS.87: 3 residues within 4Å: Chain C: V.84, V.85, H.93 Ligand excluded by PLIP DMS.88: 2 residues within 4Å: Chain C: K.621, W.717 Ligand excluded by PLIP DMS.89: 3 residues within 4Å: Chain C: L.250, R.251, D.252 Ligand excluded by PLIP DMS.90: 6 residues within 4Å: Chain C: F.231, N.232, D.233, F.235, E.334, R.336 Ligand excluded by PLIP DMS.91: 4 residues within 4Å: Chain B: W.474, V.478 Chain C: D.428, P.430 Ligand excluded by PLIP DMS.92: 3 residues within 4Å: Chain C: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.93: 7 residues within 4Å: Chain C: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.73 Ligand excluded by PLIP DMS.94: 6 residues within 4Å: Chain C: W.36, D.45, R.46, P.47, S.48 Ligands: DMS.78 Ligand excluded by PLIP DMS.95: 4 residues within 4Å: Chain C: R.37, S.132, W.133, H.216 Ligand excluded by PLIP DMS.96: 4 residues within 4Å: Chain C: N.102, D.598, F.601, V.795 Ligand excluded by PLIP DMS.97: 3 residues within 4Å: Chain C: Q.266, V.267, A.268 Ligand excluded by PLIP DMS.108: 9 residues within 4Å: Chain D: T.229, V.330, G.331, R.333, R.448, N.449, H.450, P.451, R.482 Ligand excluded by PLIP DMS.109: 5 residues within 4Å: Chain D: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.110: 5 residues within 4Å: Chain D: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.111: 7 residues within 4Å: Chain D: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligand excluded by PLIP DMS.112: 3 residues within 4Å: Chain D: T.271, L.291, R.292 Ligand excluded by PLIP DMS.113: 4 residues within 4Å: Chain D: E.314, H.316, G.320 Ligands: DMS.128 Ligand excluded by PLIP DMS.114: 5 residues within 4Å: Chain D: L.54, N.55, G.56, E.57, L.125 Ligand excluded by PLIP DMS.115: 3 residues within 4Å: Chain D: E.334, V.335, P.480 Ligand excluded by PLIP DMS.116: 4 residues within 4Å: Chain D: P.106, P.115, W.191 Ligands: DMS.119 Ligand excluded by PLIP DMS.117: 5 residues within 4Å: Chain D: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.118: 6 residues within 4Å: Chain D: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.119: 4 residues within 4Å: Chain D: G.593, D.594, T.595 Ligands: DMS.116 Ligand excluded by PLIP DMS.120: 4 residues within 4Å: Chain D: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.121: 2 residues within 4Å: Chain D: K.621, W.717 Ligand excluded by PLIP DMS.122: 3 residues within 4Å: Chain D: L.250, R.251, D.252 Ligand excluded by PLIP DMS.123: 3 residues within 4Å: Chain D: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.124: 7 residues within 4Å: Chain D: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.106 Ligand excluded by PLIP DMS.125: 5 residues within 4Å: Chain D: A.34, W.36, D.45, R.46, P.47 Ligand excluded by PLIP DMS.126: 4 residues within 4Å: Chain D: N.102, D.598, F.601, V.795 Ligand excluded by PLIP DMS.127: 5 residues within 4Å: Chain D: S.923, Y.926, R.961, Y.962, A.978 Ligand excluded by PLIP DMS.128: 3 residues within 4Å: Chain D: G.320, L.322 Ligands: DMS.113 Ligand excluded by PLIP DMS.129: 5 residues within 4Å: Chain D: Q.49, Q.50, D.130, S.132, W.133 Ligand excluded by PLIP DMS.130: 6 residues within 4Å: Chain D: W.133, L.134, Q.135, E.136, G.137, S.174 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Juers, D.H. et al., A Structural View of the Action of Escherichia Coli (Lacz) Beta-Galactosidase. Biochemistry (2001)

Release Date

2001-12-07

Peptides

Beta-Galactosidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Beta-Galactosidase

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